@jbrowse/plugin-sequence 1.5.0 → 1.5.4

package/dist/IndexedFastaAdapter/IndexedFastaAdapter.d.ts

@@ -6,14 +6,14 @@ import { AnyConfigurationModel } from '@jbrowse/core/configuration/configuration
 import PluginManager from '@jbrowse/core/PluginManager';
 import { getSubAdapterType } from '@jbrowse/core/data_adapters/dataAdapterCache';
 export default class extends BaseFeatureDataAdapter implements SequenceAdapter {
-    protected fasta: typeof IndexedFasta;
+    protected fasta: IndexedFasta;
     private seqCache;
     constructor(config: AnyConfigurationModel, getSubAdapter?: getSubAdapterType, pluginManager?: PluginManager);
-    getRefNames(opts?: BaseOptions): any;
+    getRefNames(opts?: BaseOptions): Promise<string[]>;
     getRegions(opts?: BaseOptions): Promise<{
         refName: string;
         start: number;
-        end: any;
+        end: number;
     }[]>;
     /**
      * Fetch features for a certain region

package/dist/TwoBitAdapter/TwoBitAdapter.d.ts

@@ -9,7 +9,7 @@ export default class TwoBitAdapter extends BaseFeatureDataAdapter implements Seq
     protected chromSizesData: Promise<Record<string, number> | undefined>;
     private initChromSizes;
     constructor(config: AnyConfigurationModel, getSubAdapter?: getSubAdapterType, pluginManager?: PluginManager);
-    getRefNames(): Promise<any>;
+    getRefNames(): Promise<string[]>;
     getRegions(): Promise<NoAssemblyRegion[]>;
     /**
      * Fetch features for a certain region

package/dist/plugin-sequence.cjs.development.js

@@ -10,6 +10,7 @@ var FeatureRendererType = _interopDefault(require('@jbrowse/core/pluggableElemen
 var TrackType = _interopDefault(require('@jbrowse/core/pluggableElementTypes/TrackType'));
 var Plugin = _interopDefault(require('@jbrowse/core/Plugin'));
 var pluginLinearGenomeView = require('@jbrowse/plugin-linear-genome-view');
+var tracks = require('@jbrowse/core/util/tracks');
 var configuration = require('@jbrowse/core/configuration');
 var color = require('@jbrowse/core/util/color');
 var ui = require('@jbrowse/core/ui');
@@ -32,14 +33,9 @@ function ownKeys(object, enumerableOnly) {
 
   if (Object.getOwnPropertySymbols) {
     var symbols = Object.getOwnPropertySymbols(object);
-
-    if (enumerableOnly) {
-      symbols = symbols.filter(function (sym) {
-        return Object.getOwnPropertyDescriptor(object, sym).enumerable;
-      });
-    }
-
-    keys.push.apply(keys, symbols);
+    enumerableOnly && (symbols = symbols.filter(function (sym) {
+      return Object.getOwnPropertyDescriptor(object, sym).enumerable;
+    })), keys.push.apply(keys, symbols);
   }
 
   return keys;
@@ -47,19 +43,12 @@ function ownKeys(object, enumerableOnly) {
 
 function _objectSpread2(target) {
   for (var i = 1; i < arguments.length; i++) {
-    var source = arguments[i] != null ? arguments[i] : {};
-
-    if (i % 2) {
-      ownKeys(Object(source), true).forEach(function (key) {
-        _defineProperty(target, key, source[key]);
-      });
-    } else if (Object.getOwnPropertyDescriptors) {
-      Object.defineProperties(target, Object.getOwnPropertyDescriptors(source));
-    } else {
-      ownKeys(Object(source)).forEach(function (key) {
-        Object.defineProperty(target, key, Object.getOwnPropertyDescriptor(source, key));
-      });
-    }
+    var source = null != arguments[i] ? arguments[i] : {};
+    i % 2 ? ownKeys(Object(source), !0).forEach(function (key) {
+      _defineProperty(target, key, source[key]);
+    }) : Object.getOwnPropertyDescriptors ? Object.defineProperties(target, Object.getOwnPropertyDescriptors(source)) : ownKeys(Object(source)).forEach(function (key) {
+      Object.defineProperty(target, key, Object.getOwnPropertyDescriptor(source, key));
+    });
   }
 
   return target;
@@ -120,6 +109,9 @@ function _defineProperties(target, props) {
 function _createClass(Constructor, protoProps, staticProps) {
   if (protoProps) _defineProperties(Constructor.prototype, protoProps);
   if (staticProps) _defineProperties(Constructor, staticProps);
+  Object.defineProperty(Constructor, "prototype", {
+    writable: false
+  });
   return Constructor;
 }
 
@@ -143,12 +135,15 @@ function _inherits(subClass, superClass) {
     throw new TypeError("Super expression must either be null or a function");
   }
 
-  subClass.prototype = Object.create(superClass && superClass.prototype, {
-    constructor: {
-      value: subClass,
-      writable: true,
-      configurable: true
-    }
+  Object.defineProperty(subClass, "prototype", {
+    value: Object.create(superClass && superClass.prototype, {
+      constructor: {
+        value: subClass,
+        writable: true,
+        configurable: true
+      }
+    }),
+    writable: false
   });
   if (superClass) _setPrototypeOf(subClass, superClass);
 }
@@ -821,6 +816,12 @@ var SequencePlugin = /*#__PURE__*/function (_Plugin) {
         return new AdapterType({
           name: 'TwoBitAdapter',
           configSchema: twoBitAdapterConfigSchema,
+          adapterMetadata: {
+            category: null,
+            hiddenFromGUI: true,
+            displayName: null,
+            description: null
+          },
           getAdapterClass: function getAdapterClass() {
             return Promise.resolve().then(function () { return TwoBitAdapter$1; }).then(function (r) {
               return r["default"];
@@ -828,10 +829,41 @@ var SequencePlugin = /*#__PURE__*/function (_Plugin) {
           }
         });
       });
+      pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', function (adapterGuesser) {
+        return function (file, index, adapterHint) {
+          var regexGuess = /\.2bit$/i;
+          var adapterName = 'TwoBitAdapter';
+          var fileName = tracks.getFileName(file);
+
+          if (regexGuess.test(fileName) || adapterHint === adapterName) {
+            return {
+              type: adapterName,
+              twoBitLocation: file
+            };
+          }
+
+          return adapterGuesser(file, index, adapterHint);
+        };
+      });
+      pluginManager.addToExtensionPoint('Core-guessTrackTypeForLocation', function (trackTypeGuesser) {
+        return function (adapterName) {
+          if (adapterName === 'TwoBitAdapter') {
+            return 'ReferenceSequenceTrack';
+          }
+
+          return trackTypeGuesser(adapterName);
+        };
+      });
       pluginManager.addAdapterType(function () {
         return new AdapterType({
           name: 'ChromSizesAdapter',
           configSchema: chromSizesAdapterConfigSchema,
+          adapterMetadata: {
+            category: null,
+            hiddenFromGUI: true,
+            displayName: null,
+            description: null
+          },
           getAdapterClass: function getAdapterClass() {
             return Promise.resolve().then(function () { return ChromSizesAdapter; }).then(function (r) {
               return r["default"];
@@ -843,6 +875,12 @@ var SequencePlugin = /*#__PURE__*/function (_Plugin) {
         return new AdapterType({
           name: 'IndexedFastaAdapter',
           configSchema: indexedFastaAdapterConfigSchema,
+          adapterMetadata: {
+            category: null,
+            hiddenFromGUI: true,
+            displayName: null,
+            description: null
+          },
           getAdapterClass: function getAdapterClass() {
             return Promise.resolve().then(function () { return IndexedFastaAdapter; }).then(function (r) {
               return r["default"];
@@ -850,10 +888,42 @@ var SequencePlugin = /*#__PURE__*/function (_Plugin) {
           }
         });
       });
+      pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', function (adapterGuesser) {
+        return function (file, index, adapterHint) {
+          var regexGuess = /\.(fa|fasta|fas|fna|mfa)$/i;
+          var adapterName = 'IndexedFastaAdapter';
+          var fileName = tracks.getFileName(file);
+
+          if (regexGuess.test(fileName) || adapterHint === adapterName) {
+            return {
+              type: adapterName,
+              fastaLocation: file,
+              faiLocation: index || tracks.makeIndex(file, '.fai')
+            };
+          }
+
+          return adapterGuesser(file, index, adapterHint);
+        };
+      });
+      pluginManager.addToExtensionPoint('Core-guessTrackTypeForLocation', function (trackTypeGuesser) {
+        return function (adapterName) {
+          if (adapterName === 'IndexedFastaAdapter') {
+            return 'ReferenceSequenceTrack';
+          }
+
+          return trackTypeGuesser(adapterName);
+        };
+      });
       pluginManager.addAdapterType(function () {
         return new AdapterType({
           name: 'BgzipFastaAdapter',
           configSchema: bgzipFastaAdapterConfigSchema,
+          adapterMetadata: {
+            category: null,
+            hiddenFromGUI: true,
+            displayName: null,
+            description: null
+          },
           getAdapterClass: function getAdapterClass() {
             return Promise.resolve().then(function () { return BgzipFastaAdapter; }).then(function (r) {
               return r["default"];
@@ -861,9 +931,41 @@ var SequencePlugin = /*#__PURE__*/function (_Plugin) {
           }
         });
       });
+      pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', function (adapterGuesser) {
+        return function (file, index, adapterHint) {
+          var regexGuess = /\.(fa|fasta|fas|fna|mfa)\.b?gz$/i;
+          var adapterName = 'BgzipFastaAdapter';
+          var fileName = tracks.getFileName(file);
+
+          if (regexGuess.test(fileName) || adapterHint === adapterName) {
+            return {
+              type: adapterName,
+              faiLocation: tracks.makeIndex(file, '.fai'),
+              gziLocation: tracks.makeIndex(file, '.gzi')
+            };
+          }
+
+          return adapterGuesser(file, index, adapterHint);
+        };
+      });
+      pluginManager.addToExtensionPoint('Core-guessTrackTypeForLocation', function (trackTypeGuesser) {
+        return function (adapterName) {
+          if (adapterName === 'BgzipFastaAdapter') {
+            return 'ReferenceSequenceTrack';
+          }
+
+          return trackTypeGuesser(adapterName);
+        };
+      });
       pluginManager.addAdapterType(function () {
         return new AdapterType(_objectSpread2({
-          name: 'GCContentAdapter'
+          name: 'GCContentAdapter',
+          adapterMetadata: {
+            category: null,
+            hiddenFromGUI: true,
+            displayName: null,
+            description: null
+          }
         }, pluginManager.load(GCContentAdapterF)));
       });
       pluginManager.addTrackType(function () {
@@ -1833,7 +1935,9 @@ var default_1 = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
 
   }, {
     key: "freeResources",
-    value: function freeResources() {}
+    value: function
+      /* { region } */
+    freeResources() {}
   }]);
 
   return default_1;
@@ -2078,7 +2182,9 @@ var TwoBitAdapter = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
 
   }, {
     key: "freeResources",
-    value: function freeResources() {}
+    value: function
+      /* { region } */
+    freeResources() {}
   }]);
 
   return TwoBitAdapter;
@@ -2205,7 +2311,9 @@ var _default = /*#__PURE__*/function (_BaseAdapter) {
     }
   }, {
     key: "freeResources",
-    value: function freeResources() {}
+    value: function
+      /* { region } */
+    freeResources() {}
   }]);
 
   return _default;
@@ -2391,7 +2499,9 @@ var _default$1 = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
 
   }, {
     key: "freeResources",
-    value: function freeResources() {}
+    value: function
+      /* { region } */
+    freeResources() {}
   }]);
 
   return _default;
@@ -2438,7 +2548,7 @@ var _default$2 = /*#__PURE__*/function (_IndexedFasta) {
     return _this;
   }
 
-  return _default;
+  return _createClass(_default);
 }(_default$1);
 
 var BgzipFastaAdapter = {